Ca you help me understand the Nanopore fastqc results?

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2.5 years ago

Assa Yeroslaviz ★ 1.9k

I have a follow-up question regarding my ONT data set, after my first question here. I have used minimap2 to map my sample against the reference genome and converted the results sam into bam file. I have than ran pycoQC with the addition of the bam files to check the alignments. I have attached below a few of the additional images added with the bam file QC run.

When I look at the pie chart I get only 0.14% unmapped reads, which would have been great, but when I look at the plot below, which shows the bases alignment rate, it shows ~70% reads unmapped. How do these two results fit together?

thanks

alignment summary alignment vs. basecalled alignment length

pycoQC long-read-seq nanopore fastqc • 847 views

ADD COMMENT • link 2.5 years ago by Assa Yeroslaviz ★ 1.9k

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Is it possible to put the actual file up somplace? It is difficult to see things from this image.

ADD REPLY • link 2.5 years ago by GenoMax 147k

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yes, you can download it from the github repository.

ADD REPLY • link 2.5 years ago by Assa Yeroslaviz ★ 1.9k

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